Effects of Preprocessing on Text Classification in Balanced and Imbalanced Datasets

Mehmet F. Karaca 한국인터넷정보학회 2024 KSII Transactions on Internet and Information Syst Vol.18 No.3

In this study, preprocessings with all combinations were examined in terms of the effects on decreasing word number, shortening the duration of the process and the classification success in balanced and imbalanced datasets which were unbalanced in different ratios. The decreases in the word number and the processing time provided by preprocessings were interrelated. It was seen that more successful classifications were made with Turkish datasets and English datasets were affected more from the situation of whether the dataset is balanced or not. It was found out that the incorrect classifications, which are in the classes having few documents in highly imbalanced datasets, were made by assigning to the class close to the related class in terms of topic in Turkish datasets and to the class which have many documents in English datasets. In terms of average scores, the highest classification was obtained in Turkish datasets as follows: with not applying lowercase, applying stemming and removing stop words, and in English datasets as follows: with applying lowercase and stemming, removing stop words. Applying stemming was the most important preprocessing method which increases the success in Turkish datasets, whereas removing stop words in English datasets. The maximum scores revealed that feature selection, feature size and classifier are more effective than preprocessing in classification success. It was concluded that preprocessing is necessary for text classification because it shortens the processing time and can achieve high classification success, a preprocessing method does not have the same effect in all languages, and different preprocessing methods are more successful for different languages.

Phenotypic and Molecular Characterization of Risk Loci Associated With Asthma and Lung Function

Mehmet Karaca,Nazente Atceken,Şefayet Karaca,Ersoy Civelek,Bülent E. Şekerel,Renato Polimanti 대한천식알레르기학회 2020 Allergy, Asthma & Immunology Research Vol.12 No.5

Purpose: Respiratory diseases have a highly multifactorial etiology where different mechanisms contribute to the individual's susceptibility. We conducted a deep characterization of loci associated with asthma and lung function by previous genome-wide association studies (GWAS). Methods: Sixteen variants were selected from previous GWAS of childhood/adult asthma and pulmonary function tests. We conducted a phenome-wide association study of these loci in 4,083 traits assessed in the UK Biobank (n = 361,194 participants). Data from the Genotype-Tissue Expression (GTEx) project were used to conduct a transcriptomic analysis with respect to tissues relevant for asthma pathogenesis. A pediatric cohort assessed with the International Study of Asthma and Allergies in Children (ISAAC) Phase II tools was used to further explore the association of these variants with 116 traits related to asthma comorbidities. Results: Our phenome-wide association studies (PheWAS) identified 206 phenotypic associations with respect to the 16 variants identified. In addition to the replication of the phenotypes tested in the discovery GWAS, we observed novel associations related to blood levels of immune cells (eosinophils, neutrophils, monocytes, and lymphocytes) for the asthma-related variants. Conversely, the lung-function variants were associated with phenotypes related to body fat mass. In the ISAAC-assessed cohort, we observed that risk alleles associated with increased fat mass can exacerbate allergic reactions in individuals affected by allergic respiratory diseases. The GTEx-based analysis showed that the variants tested affect the transcriptomic regulation of multiple surrounding genes across several tissues. Conclusions: This study generated novel data regarding the genetics of respiratory diseases and their comorbidities, providing a deep characterization of loci associated with asthma and lung function.

Intraoperative Halo-Femoral Traction in Surgical Treatment of Adolescent Idiopathic Scoliosis Curves between 70° and 90°: Is It Effective?

Mehmet Nuri Erdem,Ismail Oltulu,Sinan Karaca,Seçkin Sari,Mehmet Aydogan 대한척추외과학회 2018 Asian Spine Journal Vol.12 No.4

Study Design: A retrospective clinical study. Purpose: To analyze the surgical outcomes of intraoperative halo-femoral traction (HFT) in patients with adolescent idiopathic scoliosis (AIS) with Cobb angles between 70° and 90° and flexibility <35%. Overview of Literature: Numerous methods have been described to achieve adequate correction and successful results in the surgical treatment of AIS patients with a Cobb angle >70°. However, few studies have evaluated the results of HFT in AIS patients with Cobb angles between 70° and 90° and flexibility <35%. Methods: The study comprised 24 AIS patients (18 females, six males; mean age, 17.4 years; mean preoperative Cobb angle, 80.1°; range, 70°–90°) who underwent surgery using intraoperative HFT. Neurological status was constantly assessed during the surgery using intraoperative neurophysiological monitoring. Results: The mean follow-up period was 33.5 months. Radiographic outcomes demonstrated 85.7% correction of the major Cobb angle. Coronal and sagittal balance was achieved in all the patients, and shoulder levels were equalized. The traction was discontinued when a decrease in spinal cord potentials was observed during the surgery. Conclusions: Intraoperative HFT is an effective and reliable method for the management of scoliosis curves between 70° and 90°. The most significant advantages of the method are avoidance of the morbidities related to anterior surgery, osteotomy, or vertebral column resection; its contribution in helping achieve adequate reduction and optimum balance by the gradually increased corrective force, lack of any need for extreme correction force during instrumentation; and the high correction rates achieved.

The effect of mesenchymal stem cell use on intraabdominal adhesions in a rat model

Gokhan Karaca,Faruk Pehlivanli,Oktay Aydin,Canan Altunkaya,Hafize Uzun,Mehmet Niyaz,Huseyin Ozden,Huri Bulut 대한외과학회 2018 Annals of Surgical Treatment and Research(ASRT) Vol.94 No.2

Purpose: Intra-abdominal adhesions (IAA) are among the most frequently seen pathologies in general surgery practice with an increased morbidity and mortality. In the present study, we investigated the effect of locally applied mesenchymal stem cells (MSCs) on IAA. Methods: Twenty-four Wistar Albino rats were used in the study. The rats were divided into three groups including: Sham, control, and MSCs group. On day 0, cecum was reached under anesthesia in all groups, except the Sham group. Scraping with a sponge was performed until petechial bleeding occurred. The control group received no treatment. In the stem cell group, MSCs were applied topically immediately after surgery on adhesions. The rats were sacrificed on day 10 and colon tissues and blood samples were collected for macroscopic, histopathological, and biochemical analysis. Results: In our study, E-selectin, P-selectin, TNF-α and IL-1 levels were statistically significantly lower in the MSC group than the control group, while the sham group has the lowest levels. In both the macroscopic and histopathological analyses (Zühlke’s scale), the least amount of adhesion was observed in the Sham group. In addition, although there was less adhesion in the MSC group than the control group, the difference did not reach statistical significance. Conclusion: Topical MSC application immediately after surgery suppresses the inflammatory process. However it was found to be ineffective in histopathological and macroscopic examinations performed on the 10th day.

Acute pulmonary thromboemboli due to a giant mobile thrombus

Ataman Köse,Mehmet Kerem Karaca,Ahmet Celik,Serdar Biricik,Murat Ozeren 대한응급의학회 2017 Clinical and Experimental Emergency Medicine Vol.4 No.2

Weekly Topotecan for Recurrent Small Cell Lung Cancer - a Retrospective Anatolian Medical Oncology Group Study

Altinbas, Mustafa,Kalender, Mehmet Emin,Oven, Basak,Sevinc, Alper,Karaca, Halit,Kaplan, M. Ali,Alici, Suleyman,Arpaci, Erkan,Yildiz, Ramazan,Uncu, Dogan,Camci, Celalettin,Gumus, Mahmut Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.6

Aim: To evaluate efficacy and tolerability of topotecan treatment for recurrent small cell lung carcinoma. Patients and Methods: A total of 62 patients were evaluated retrospectively. Statistical analysis was performed using GraphPad Instat (version 3.05). Results: DFifty five of patients (89%) were male and 7 (11%) were female. Median age was $56.7{\pm}9.3$ (34-75). Forty eight of patients (80%) were extensive stage (ES) at the time of diagnosis. Fifty of the patients (80.6 Medical Oncology Clinic) were given median 5.36 cycles of cisplatin-etoposide (2-8 cycles). Time to recurrence was $15.6{\pm}6.13$ weeks in patients with limited stage (LS) and $6.3{\pm}3.82$ weeks in extensive stage (ES) (p<0.0001). Overall survival was $14.0{\pm}6.08$ months in ES and $17.9{\pm}6.88$ months in LS. The difference between two groups was statistically meaningful (p=0.0447). The overall survival of the patients was $14.8{\pm}6.43$ months (4.5-40 months). In terms of survival, there was no difference between males and females (p=0.1171). In 17 (27%) patients who were refractory to topotecan or in whom progression occurred other chemotherapies were used. Conclusion: Small cell lung cancer is chemosensitive, but recurrences occur in short time. Other chemotherapy regimens are used in progression. Topotecan is one of them. Patients who were young and in whom recurrences occur late had given better response to topotecan. Because of the retrospective nature of the study, we couldn't reach the records exactly and consequently, rate and duration of response couldn't be calculated. In recurrent SCLC topotecan is one of the treatment choices. But both hematological and non hematological side effects should be taken into consideration.

XELOX Plus Bevacizumab vs. FOLFIRI Plus Bevacizumab Treatment for First-line Chemotherapy in Metastatic Colon Cancer: a Retrospective Study of the Anatolian Society of Medical Oncology

Duran, Ayse Ocak,Karaca, Halit,Besiroglu, Mehmet,Bayoglu, Ibrahim Vedat,Menekse, Serkan,Yapici, Heves Surmeli,Yazilitas, Dogan,Bahceci, Aykut,Uysal, Mukremin,Sevinc, Alper,Hacibekiroglu, Ilhan,Aksoy, Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.23

Background: XELOX plus bevacizumab (XELOX-Bev) and FOLFIRI plus Bevacizumab (FOLFIRI - Bev) treatments are an effective strategies patients with metastatic colorectal cancer (mCRC).The aim of this study was to compare efficacy of first-line XELOX-Bev treatment vs FOLFIRI-Bev treatment for mCRC. Materials and Methods: A total of 409 patients with mCRC who received chemotherapy were included and divided into 2 groups. Group 1 (n=298) received XELOX-Bev and Group 2 (n=111) FOLFIRI-Bev. Comparisons were made in terms of overall (OS) and progression-free (PFS) survival, response rate (RR), and grade 3-4 toxicity. Results: Median follow-up was 11 months in Group 1 and 15 months for Group 2. Complete remission was observed in 29 (9.7%) and 2 (1.8%) patients, partial remission in 139 (46.6%) and 27 (24.5%), stable disease in 88 (29.5%) and 49 (44.1%) and progressive disease in 42 (14.1%) and 33 (30.0%) patients in Group 1 and 2, respectively. Median OS was 25 months (range 2-57 months, 95%CI; 22.2-27.7) for Group 1 and 20 months (range 1-67 months, 95%CI; 16.8-23.1) for Group 2 (p=0.036). Median PFS was 9.6 months (range 2-36 months, 95%CI; 8.8-10.4) for Group 1 and 9 months (range 1-44 months, 95%CI; 7.4-10.5) for Group 2 (p=0.019). Objective RR was 56.4% in Group 1 and 26.1% in Group 2 (p<0.001). Conclusions: First-line XELOX-Bev is more effective with a better response rate, prolongation of median PFS/OS, and a superior safety profile compared with FOLFIRI-Bev.

Efficacy of Dose Dense Doxorubicin and Cyclophosphamide Followed by Paclitaxel versus Conventional Dose Doxorubicin, Cyclophosphamide Followed by Paclitaxel or Docetaxel in Patients with Node-Positive Breast Cancer

Yazilitas, Dogan,Sendur, Mehmet Ali Nahit,Karaca, Halit,Ozdemir, Nuriye,Aksoy, Sercan,Berk, Veli,Yazici, Ozan,Ozturk, Banu,Ozkan, Metin,Zengin, Nurullah,Altundag, Kadri Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.4

Background: Adding taxanes to adjuvant antracycline and cyclophosphamide (AC) in combination may provide significant improvement in node-positive and high risk node-negative breast cancer (BC) patients. However, the optimal dose and the role of dose-dense (DD) chemotherapy have yet to be determined. The aim of this study was to compare the efficacy of a DD paclitaxel (P)-AC combination with conventional weekly P-AC or docetaxel D-AC combinations in patients with node-positive breast cancer. Materials and Methods: Newly diagnosed 280 node-positive BC patients diagnosed from 1998 to 2013 in three clinics were retrospectively analyzed. Demographic and medical data were collected from the medical charts. Patients were categorized to 3 groups according to treatment arms: arm A, ddAC-P; arm B, weekly P and AC combination; and arm C; T and AC combination. Adjuvant trastuzumab was added for HER2-positive patients. Kaplan-Meier survival analysis was carried out for disease free survival (DFS) and overall survival (OS). The log-rank test was used to examine the statistical significance of the differences observed between the groups. Two-sided P values <0.05 were considered statistically significant. Results: Of the total of 280 patients, 101 were in arm A, 114 in arm B and 65 in arm C.The median ages were 49, 50 and 46, respectively (p=0.11). Median follow-up was 39 (3-193) months. Stage, lymphovascular and perineural invasion, receptor patern, and menopausal status were similar in the 3 treatment arms, but HER2 positivity was significantly lower in arm A, compared to arms B and C (25.7%, 53.1%, 41.5% in arms A, B and C, respectively; p<0.001). Also grade 3 tumors were significantly less frequent in treatment arm A compared to arm B and C (27.3%, 56.8% and 49.2%, respectively, p=0.01). Afterunivariate and multivariate analysis were performed, 3-year DFS rates were 89%, 81%, and 75%, respectively (p=0.12) and three year OS rates were 96.6%, 89%, and 75% (p=0.62). Conclusions: In this study, no significant difference was found between adjuvant dose dense and conventional taxane treatment regimens.

Species-Specific DNA Markers in Genus Capsicum

Naci Onus,Ayse Gul. Ince,Mehmet Karaca 한국원예학회 2006 한국원예학회 기타간행물 Vol.- No.-

Roles for Paraoxonase but not Ceruloplasmin in Peritoneal Washing Fluid in Differential Diagnosis of Gynecologic Pathologies

Yildirim, Mustafa,Demirpence, Ozlem,Kaya, Vildan,Suren, Dinc,Karaca, Mehmet,Evliyaoglu, Osman,Yilmaz, Necat,Gunduz, Seyda Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.15

Background: Intraperitoneal spread of gynecologic cancers is a major cause of mortality and morbidity and often presents with malignant ascites. Microscopic tumor spread can be demonstrated by a peritoneal wash cytology and help assess the prognosis of the disease. In our study, the roles of paraoxonase and ceruloplasmin, measured in peritoneal washing fluid of patients operated for gynecologic pathologies in differential diagnosis was investigated. Materials and Methods: Patients operated for malign or benign gynecologic pathologies in Antalya Education and Research Hospital Gynecology Clinic between 2010-2012 were included in the study. Samples were obtained during surgery. Results: A statistically significant difference was detected between patients with benign and malign diseases with regards to PON1 levels measured in peritoneal washing fluid (p:0.044), the average values being $64.2{\pm}30.8$ (Range 10.8-187.2) and $41.4{\pm}21.4$ (Range 10.4-95.5), respectively. No significant variation was evident for ceruloplasmin. Conclusions: Paraoxonase levels measured in peritoneal washing fluid may contribute to the differentiation of malign-benign diseases in gynecologic pathologies.